Quick start: A user guide

1. Introduction

  • “Microglia Analyzer” is a Python module allowing to segment, classify and measure microglia from 2D fluo images.

  • This module is also a Napari plugin in case you would need a graphical interface.

  • The segmentation produced doesn’t allow to recover the actual surface of microglia since the output of the segmentation is a shape optimized for skeletonization.

  • Each cell is classified according 3 classes: “amoeboid”, “intermediate” and “homeostatic”.

  • The measures (bundled in a CSV file by the end) include:

    • The total length of each cell

    • The number of junctions for each cell

    • The number of leaves for each cell

    • The average branch length for each cell

  • From the GUI (Napari), a batch mode is available allowing you run the whole workflow over an entire folder.

_images/overview.png

2. Install the plugin

  • We strongly recommand to use conda or any other virtual environment manager instead of installing Napari and microglia-analyzer in your system’s Python.

  • Napari is only required if you want to use microglia-analyzer with a graphical interface.

  • Napari is not part of microglia-analyzer’s dependencies, so you will have to install it separately.

  • Each of the commands below is supposed to be ran after you activated your virtual environment.

  • If the install was successful, you should see the plugin in Napari in the top bar menu: Plugins > Microglia Analyzer > Microglia Analyzer.

A. Development versions

Method

Instructions

pip

pip install git+https://github.com/MontpellierRessourcesImagerie/microglia-analyzer.git

GitHub

pip install git+https://github.com/MontpellierRessourcesImagerie/microglia-analyzer.git.

From an archive

  • Download the archive pyproject.toml and launch pip install -e ..

  • From the terminal containing your virtual env, move to the folder containing the file pyproject.toml

  • Run the command pip install -e .

B. Stable versions

Method

Instructions

pip

Activate your conda environment, and type pip install microglia-analyzer.

NapariHub

Go in the plugins menu of Napari and search for “Microglia Analyzer”

3. Notes

  • The plugin provides detailed output, so it’s recommended to monitor the terminal if you want detailed information about its actions.

  • If a crash occurs, please create an issue and include the relevant image(s) and a copy of your terminal for further investigation.

  • Napari currently supports only open file formats, so make sure to convert your images to TIFF format before using them with Napari.

4. Quick start

Features